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- PDB-6f9z: Lysozyme crystallized in presence of 5 mM ammonium sulphate at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 6f9z
TitleLysozyme crystallized in presence of 5 mM ammonium sulphate at pH 4.5
ComponentsLysozyme C
KeywordsHYDROLASE
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding.
Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1923
Polymers14,0611
Non-polymers1322
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-21 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.009, 56.132, 72.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14060.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.11 % / Mosaicity: 0.3 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5 mM Ammonium Sulphate, 0.4 M Sodium Chloride, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2017 / Details: Compound Refractive Lens
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.2→19.72 Å / Num. obs: 37901 / % possible obs: 97.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 12.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.02 / Rrim(I) all: 0.041 / Net I/σ(I): 15.5 / Num. measured all: 146195
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.220.45419100.8030.2670.52997.9
6.46-19.720.0222860.9990.0120.02595.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E3U

4e3u


Resolution: 1.2→19.719 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 17.89
RfactorNum. reflection% reflection
Rfree0.1777 3538 5.06 %
Rwork0.1563 --
obs0.1574 37845 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.76 Å2 / Biso mean: 17.5061 Å2 / Biso min: 9.31 Å2
Refinement stepCycle: final / Resolution: 1.2→19.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 6 183 1170
Biso mean--45.03 28.26 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131069
X-RAY DIFFRACTIONf_angle_d1.1421456
X-RAY DIFFRACTIONf_chiral_restr0.092149
X-RAY DIFFRACTIONf_plane_restr0.008191
X-RAY DIFFRACTIONf_dihedral_angle_d21.051403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21640.21351670.22112497266492
1.2164-1.23380.25051210.21062686280795
1.2338-1.25220.28011310.20272802293398
1.2522-1.27180.25941410.20562703284497
1.2718-1.29260.18671400.20012695283597
1.2926-1.31490.21711260.18762734286097
1.3149-1.33880.23871430.18642749289297
1.3388-1.36460.22531530.18262738289198
1.3646-1.39240.22371220.17762702282497
1.3924-1.42270.18311200.16382758287897
1.4227-1.45580.22811510.1632687283898
1.4558-1.49220.19191530.14992736288997
1.4922-1.53250.20991020.15431675177761
1.5325-1.57760.19091670.13782635280294
1.5776-1.62850.1741270.14042593272093
1.6285-1.68670.15041360.13962751288798
1.6867-1.75410.19651350.14272775291098
1.7541-1.83390.1451670.14892674284197
1.8339-1.93050.22121640.14942708287297
1.9305-2.05140.17331400.15382711285197
2.0514-2.20960.20131290.14022706283596
2.2096-2.43160.15191640.14212654281895
2.4316-2.78260.12831300.15122574270492
2.7826-3.50260.17481640.15582650281495
3.5026-19.72140.1651450.15822756290198

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